git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10611 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/citeme.cpp

@@ -40,13 +40,16 @@ CiteMe::CiteMe(LAMMPS *lmp) : Pointers(lmp)
 
 CiteMe::~CiteMe()
 {
-  if (universe->me) return;
-  if (cs->size() == 0) return;
+  if (universe->me || cs->size() == 0) {
+    delete cs;
+    return;
+  }
+
+  delete cs;
 
   if (screen) fprintf(screen,cite_nagline);
   if (logfile) fprintf(logfile,cite_nagline);
 
-  delete cs;
   if (fp) fclose(fp);
 }
 

src/fix.cpp

@@ -58,6 +58,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   time_depend = 0;
   create_attribute = 0;
   restart_pbc = 0;
+  wd_header = wd_section = 0;
   cudable_comm = 0;
 
   scalar_flag = vector_flag = array_flag = 0;

src/fix.h

@@ -43,6 +43,8 @@ class Fix : protected Pointers {
                                  //      setting when a new atom is created
   int restart_pbc;               // 1 if fix moves atoms (except integrate)
                                  //      so write_restart must remap to PBC
+  int wd_header;                 // # of header values fix writes to data file
+  int wd_section;                // # of sections fix writes to data file
   int cudable_comm;              // 1 if fix has CUDA-enabled communication
 
   int scalar_flag;               // 0/1 if compute_scalar() function exists
@@ -165,6 +167,12 @@ class Fix : protected Pointers {
   virtual void read_data_section(char *, int, char *) {}
   virtual bigint read_data_skip_lines(char *) {return 0;}
 
+  virtual void write_data_header(FILE *, int) {}
+  virtual void write_data_section_size(int, int &, int &) {}
+  virtual void write_data_section_pack(int, double **) {}
+  virtual void write_data_section_keyword(int, FILE *) {}
+  virtual void write_data_section(int, FILE *, int, double **, int) {}
+
   virtual int modify_param(int, char **) {return 0;}
   virtual void *extract(const char *, int &) {return NULL;}
 

src/fix_property_atom.cpp

@@ -33,6 +33,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   if (narg < 4) error->all(FLERR,"Illegal fix property/atom command");
 
   restart_peratom = 1;
+  wd_section = 1;
 
   int iarg = 3;
   nvalue = narg-iarg;
@@ -150,7 +151,7 @@ void FixPropertyAtom::init()
 }
 
 /* ----------------------------------------------------------------------
-   unpack section of data file
+   unpack N lines in buf from section of data file labeled by keyword
 ------------------------------------------------------------------------- */
 
 void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
@@ -209,13 +210,95 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
   delete [] values;
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   return # of lines in section of data file labeled by keyword
+------------------------------------------------------------------------- */
 
 bigint FixPropertyAtom::read_data_skip_lines(char *keyword)
 {
   return atom->natoms;
 }
 
+/* ----------------------------------------------------------------------
+   return size I own for Mth data section
+   # of data sections = 1 for this fix
+   nx = # of local atoms
+   ny = columns = tag + nvalues
+------------------------------------------------------------------------- */
+
+void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny)
+{
+  nx = atom->nlocal;
+  ny = nvalue + 1;
+}
+
+/* ----------------------------------------------------------------------
+   pack values for Mth data section into buf
+   buf allocated by caller as Nlocal by Nvalues+1
+------------------------------------------------------------------------- */
+
+void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
+{
+  int i;
+
+  // 1st column = atom tag
+  // rest of columns = per-atom values
+
+  int *tag = atom->tag;
+  int nlocal = atom->nlocal;
+
+  for (i = 0; i < nlocal; i++) buf[i][0] = tag[i];
+
+  for (int m = 0; m < nvalue; m++) {
+    int mp1 = m+1;
+    if (style[m] == MOLECULE) {
+      int *molecule = atom->molecule;
+      for (i = 0; i < nlocal; i++) buf[i][mp1] = molecule[i];
+    } else if (style[m] == INTEGER) {
+      int *vec = atom->ivector[index[m]];
+      for (i = 0; i < nlocal; i++) buf[i][mp1] = vec[i];
+    } else if (style[m] == DOUBLE) {
+      double *vec = atom->dvector[index[m]];
+      for (i = 0; i < nlocal; i++) buf[i][mp1] = vec[i];
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   write section keyword for Mth data section to file
+   use MOLECULE if that is only field, else use fix ID
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
+{
+  if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecule\n\n");
+  else fprintf(fp,"\n%s\n\n",id);
+}
+
+/* ----------------------------------------------------------------------
+   write N lines from buf to file
+   convert buf fields to int or double depending on styles
+   index can be used to prepend global numbering
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixPropertyAtom::write_data_section(int mth, FILE *fp, 
+                                         int n, double **buf, int index)
+{
+  int m;
+
+  for (int i = 0; i < n; i++) {
+    fprintf(fp,TAGINT_FORMAT,static_cast<int> (buf[i][0]));
+    for (m = 0; m < nvalue; m++) {
+      if (style[m] == MOLECULE || style[m] == INTEGER)
+        fprintf(fp," " TAGINT_FORMAT,static_cast<int> (buf[i][m+1]));
+      else fprintf(fp," %g",buf[i][m+1]);
+    }
+    fprintf(fp,"\n");
+  }
+}
+
 /* ----------------------------------------------------------------------
    memory usage of local atom-based array
 ------------------------------------------------------------------------- */

src/fix_property_atom.h

@@ -33,6 +33,10 @@ class FixPropertyAtom : public Fix {
 
   void read_data_section(char *, int, char *);
   bigint read_data_skip_lines(char *);
+  void write_data_section_size(int, int &, int &);
+  void write_data_section_pack(int, double **);
+  void write_data_section_keyword(int, FILE *);
+  void write_data_section(int, FILE *, int, double **, int);
 
   void grow_arrays(int);
   void copy_arrays(int, int, int);

src/write_data.cpp

@@ -26,6 +26,7 @@
 #include "improper.h"
 #include "update.h"
 #include "modify.h"
+#include "fix.h"
 #include "domain.h"
 #include "universe.h"
 #include "comm.h"
@@ -106,12 +107,13 @@ void WriteData::command(int narg, char **arg)
   if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
 
   write(file);
+
   delete [] file;
 }
 
 /* ----------------------------------------------------------------------
    called from command()
-   later might let it be directly called within run/minimize loop
+   might later let it be directly called within run/minimize loop
 ------------------------------------------------------------------------- */
 
 void WriteData::write(char *file)
@@ -174,6 +176,12 @@ void WriteData::write(char *file)
   if (atom->ndihedrals) dihedrals();
   if (atom->nimpropers) impropers();
 
+  // extra sections managed by fixes
+
+  for (int i = 0; i < modify->nfix; i++)
+    if (modify->fix[i]->wd_section) 
+      for (int m = 0; m < modify->fix[i]->wd_section; m++) fix(i,m);
+
   // close data file
 
   if (me == 0) fclose(fp);
@@ -211,6 +219,11 @@ void WriteData::header()
     fprintf(fp,"%d improper types\n",atom->nimpropertypes);
   }
 
+  for (int i = 0; i < modify->nfix; i++)
+    if (modify->fix[i]->wd_header) 
+      for (int m = 0; m < modify->fix[i]->wd_header; m++) 
+        modify->fix[i]->write_data_header(fp,m);
+  
   fprintf(fp,"\n");
 
   fprintf(fp,"%-1.16e %-1.16e xlo xhi\n",domain->boxlo[0],domain->boxhi[0]);
@@ -397,7 +410,7 @@ void WriteData::bonds()
 
   int foo = atom->avec->pack_bond(buf);
 
-  // write one chunk of atoms per proc to file
+  // write one chunk of info per proc to file
   // proc 0 pings each proc, receives its chunk, writes to file
   // all other procs wait for ping, send their chunk to proc 0
 
@@ -450,7 +463,7 @@ void WriteData::angles()
 
   atom->avec->pack_angle(buf);
 
-  // write one chunk of atoms per proc to file
+  // write one chunk of info per proc to file
   // proc 0 pings each proc, receives its chunk, writes to file
   // all other procs wait for ping, send their chunk to proc 0
 
@@ -521,7 +534,7 @@ void WriteData::dihedrals()
 
   atom->avec->pack_dihedral(buf);
 
-  // write one chunk of atoms per proc to file
+  // write one chunk of info per proc to file
   // proc 0 pings each proc, receives its chunk, writes to file
   // all other procs wait for ping, send their chunk to proc 0
 
@@ -592,7 +605,7 @@ void WriteData::impropers()
 
   atom->avec->pack_improper(buf);
 
-  // write one chunk of atoms per proc to file
+  // write one chunk of info per proc to file
   // proc 0 pings each proc, receives its chunk, writes to file
   // all other procs wait for ping, send their chunk to proc 0
 
@@ -623,3 +636,56 @@ void WriteData::impropers()
 
   memory->destroy(buf);
 }
+
+/* ----------------------------------------------------------------------
+   write out Mth section of data file owned by Fix ifix
+------------------------------------------------------------------------- */
+
+void WriteData::fix(int ifix, int mth)
+{
+  // communication buffer for Fix info
+
+  int sendrow,ncol;
+  modify->fix[ifix]->write_data_section_size(mth,sendrow,ncol);
+  int maxrow;
+  MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
+
+  double **buf;
+  if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
+  else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
+
+  // pack my fix data into buf
+
+  modify->fix[ifix]->write_data_section_pack(mth,buf);
+
+  // write one chunk of info per proc to file
+  // proc 0 pings each proc, receives its chunk, writes to file
+  // all other procs wait for ping, send their chunk to proc 0
+
+  int tmp,recvrow;
+  MPI_Status status;
+  MPI_Request request;
+
+  int index = 1;
+  if (me == 0) {
+    modify->fix[ifix]->write_data_section_keyword(mth,fp);
+    for (int iproc = 0; iproc < nprocs; iproc++) {
+      if (iproc) {
+        MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request);
+        MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
+        MPI_Wait(&request,&status);
+        MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
+        recvrow /= ncol;
+      } else recvrow = sendrow;
+
+      modify->fix[ifix]->write_data_section(mth,fp,recvrow,buf,index);
+      index += recvrow;
+    }
+    
+  } else {
+    MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
+    MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world);
+  }
+
+  memory->destroy(buf);
+}

src/write_data.h

@@ -47,6 +47,7 @@ class WriteData : protected Pointers {
   void angles();
   void dihedrals();
   void impropers();
+  void fix(int, int);
 };
 
 }